Shian Su - Publications, H-index & Citations

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Shian Su

walter & eliza hall institute

22H-index

60Paper Count

6.4KCitation Count

Published Papers 15

Publication Date

stPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data

NAR GENOMICS AND BIOINFORMATICS

IF2.8

2025-12-01

OAAI

Xu, Yang; Sargeant, Callum J.; You, Yue; You, Yupei; Su, Shian; Wang, Changqing; Tian, Luyi; Chen, Yunshun; Ritchie, Matthew E.

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Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing

GENOME RESEARCH

IF5.5

2024-09-16

PREAI

Gocuk, Sena A.; Lancaster, James; Su, Shian; Jolly, Jasleen K.; Edwards, Thomas L.; Hickey, Doron G.; Ritchie, Matthew E.; Blewitt, Marnie E.; Ayton, Lauren N.; Gouil, Quentin

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scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor

genomics proteomics bioinformatics

IF2.8

2023-11-30

OAAI

Amarasinghe, Shanika L.; Yang, Phil; Voogd, Oliver; Yang, Haoyu; Du, Mei R. M.; Su, Shian; Brown, Daniel, V; Jabbari, Jafar S.; Bowden, Rory; Ritchie, Matthew E.

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Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0

genomics proteomics bioinformatics

IF2.8

2021-12-22

OAAI

Kariyawasam, Hasaru; Su, Shian; Voogd, Oliver; Ritchie, Matthew E.; Law, Charity W.

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Benchmarking UMI-based single-cell RNA-seq preprocessing workflows

GENOME BIOLOGY

IF9.4

2021-12-14

OAAI

You, Yue; Tian, Luyi; Su, Shian; Dong, Xueyi; Jabbari, Jafar S.; Hickey, Peter F.; Ritchie, Matthew E.

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Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

GENOME BIOLOGY

IF9.4

2021-11-11

OAAI

Tian, Luyi; Jabbari, Jafar S.; Thijssen, Rachel; Gouil, Quentin; Amarasinghe, Shanika L.; Voogd, Oliver; Kariyawasam, Hasaru; Du, Mei R. M.; Schuster, Jakob; Wang, Changqing; Su, Shian; Dong, Xueyi; Law, Charity W.; Lucattini, Alexis; Prawer, Yair David Joseph; Collar-Fernandez, Coralina; Chung, Jin D.; Naim, Timur; Chan, Audrey; Ly, Chi Hai; Lynch, Gordon S.; Ryall, James G.; Anttila, Casey J. A.; Peng, Hongke; Anderson, Mary Ann; Flensburg, Christoffer; Majewski, Ian; Roberts, Andrew W.; Huang, David C. S.; Clark, Michael B.; Ritchie, Matthew E.

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CD36 family members are TCR-independent ligands for CD1 antigen-presenting molecules

SCIENCE IMMUNOLOGY

IF16.3

2021-06-15

OAAI

Gherardin, Nicholas A.; Redmond, Samuel J.; McWilliam, Hamish E. G.; Almeida, Catarina F.; Gourley, Katherine H. A.; Seneviratna, Rebecca; Li, Shihan; De Rose, Robert; Ross, Fiona J.; Nguyen-Robertson, Catriona, V; Su, Shian; Ritchie, Matthew E.; Villadangos, Jose A.; Moody, D. Branch; Pellicci, Daniel G.; Uldrich, Adam P.; Godfrey, Dale, I

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Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development

IMMUNITY

IF26.3

2021-06-01

OAAI

Tian, Luyi; Tomei, Sara; Schreuder, Jaring; Weber, Tom S.; Amann-Zalcenstein, Daniela; Lin, Dawn S.; Tran, Jessica; Audiger, Cindy; Chu, Mathew; Jarratt, Andrew; Willson, Tracy; Hilton, Adrienne; Pang, Ee Shan; Patton, Timothy; Kelly, Madison; Su, Shian; Gouil, Quentin; Diakumis, Peter; Bahlo, Melanie; Sargeant, Toby; Kats, Lev M.; Hodgkin, Philip D.; O'Keeffe, Meredith; Ng, Ashley P.; Ritchie, Matthew E.; Naik, Shalin H.

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The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools

genomics proteomics bioinformatics

IF2.8

2021-04-26

OAAI

Dong, Xueyi; Tian, Luyi; Gouil, Quentin; Kariyawasam, Hasaru; Su, Shian; De Paoli-Iseppi, Ricardo; Prawer, Yair David Joseph; Clark, Michael B.; Breslin, Kelsey; Iminitoff, Megan; Blewitt, Marnie E.; Law, Charity W.; Ritchie, Matthew E.

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Covering all your bases: incorporating intron signal from RNA-seq data

genomics proteomics bioinformatics

IF2.8

2020-09-22

OAAI

Lee, Stuart; Zhang, Albert Y.; Su, Shian; Ng, Ashley P.; Holik, Aliaksei Z.; Asselin-Labat, Marie-Liesse; Ritchie, Matthew E.; Law, Charity W.

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Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal

NATURE COMMUNICATIONS

IF15.7

2020-05-15

OAAI

Lau, Kevin X.; Mason, Elizabeth A.; Kie, Joshua; De Souza, David P.; Kloehn, Joachim; Tull, Dedreia; McConville, Malcolm J.; Keniry, Andrew; Beck, Tamara; Blewitt, Marnie E.; Ritchie, Matthew E.; Naik, Shalin H.; Zalcenstein, Daniela; Korn, Othmar; Su, Shian; Romero, Irene Gallego; Spruce, Catrina; Baker, Christopher L.; McGarr, Tracy C.; Wells, Christine A.; Pera, Martin F.

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Opportunities and challenges in long-read sequencing data analysis

GENOME BIOLOGY

IF9.4

2020-02-07

869

OAAI

Amarasinghe, Shanika L.; Su, Shian; Dong, Xueyi; Zappia, Luke; Ritchie, Matthew E.; Gouil, Quentin

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Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

NATURE METHODS

IF32.1

2019-05-27

211

OAAI

Tian, Luyi; Dong, Xueyi; Freytag, Saskia; Le Cao, Kim-Anh; Su, Shian; JalalAbadi, Abolfazl; Amann-Zalcenstein, Daniela; Weber, Tom S.; Seidi, Azadeh; Jabbari, Jafar S.; Naik, Shalin H.; Ritchie, Matthew E.

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Deciphering the Innate Lymphoid Cell Transcriptional Program

CELL REPORTS

IF6.9

2016-10-01

129

OAAI

Seillet, Cyril; Mielke, Lisa A.; Amann-Zalcenstein, Daniela B.; Su, Shian; Gao, Jerry; Almeida, Francisca F.; Shi, Wei; Ritchie, Matthew E.; Naik, Shalin H.; Huntington, Nicholas D.; Carotta, Sebastian; Belz, Gabrielle T.

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Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

NUCLEIC ACIDS RESEARCH

IF13.1

2015-04-29

381

OAAI

Liu, Ruijie; Holik, Aliaksei Z.; Su, Shian; Jansz, Natasha; Chen, Kelan; Leong, Huei San; Blewitt, Marnie E.; Asselin-Labat, Marie-Liesse; Smyth, Gordon K.; Ritchie, Matthew E.

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Research Directions